Graphical Display of Pairwise Linkage Disequilibria Between SNPs

Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The methods are described in Shin et al. (2006) . Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages < https://bioconductor.org>.


Reference manual

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install.packages("LDheatmap")

1.0-6 by Brad McNeney, 4 years ago


https://sfustatgen.github.io/LDheatmap/


Browse source code at https://github.com/cran/LDheatmap


Authors: Ji-Hyung Shin [aut] , Sigal Blay [aut] , Nicholas Lewin-Koh [ctb] , Brad McNeney [aut, cre] , Gloria Yang [ctb] , Matthew Reyers [ctb] , Youwei Yan [ctb] , Jinko Graham [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports grid, genetics, snpStats, Rcpp

Suggests rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, lattice, ggplot2, vcfR, RColorBrewer

Linking to Rcpp


See at CRAN